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At ASHG, Ion Torrent Drums Up Interest; Provides Preliminary Specs for PGM


By Julia Karow

This article was originally published Nov. 5.

WASHINGTON, DC – Ion Torrent revealed some preliminary specs for its Personal Genome Sequencer, due to be launched later this year, as the Life Technologies business unit presented the instrument to potential customers at its booth at the American Society for Human Genetics meeting last week.

The speed of the instrument — a run takes approximately two hours, and several runs can be performed in a day — is what appears to be most attractive to potential customers, Maneesh Jain, Ion Torrent's vice president of marketing and business development, told In Sequence.

The first version of the PGM will sell for $49,500, plus a $16,500 server to analyze the data.

Initially, the machine will produce about 10 megabases of data per run, or about 100,000 reads of 100 base pairs each, using the so-called 314 chip, which has about 1.5 million wells and will cost $250. Reagent kits for template preparation, library preparation, and sequencing will cost another $250, bringing the total consumables cost per run to approximately $500.

In the first half of 2011, Ion Torrent plans to launch the 316 chip, with about 6 million wells, which will increase the output per run to 100 megabases and which will cost about twice as much as the 314. Additional chip upgrades will follow, with details to be revealed next year.

Sample prep, which Jain said takes about a day and can be done in batches of six to eight samples, requires an emulsion PCR protocol, which will be simplified over time. "We focused on the sequencing initially," he said, adding that the next step will be to optimize the sample prep. Life Technologies said previously that sample prep for the PGM would eventually be able to use the EZ Bead system, which was originally developed for the SOLiD system.

The data output of the instrument will be in the FASTQ format and will include base calls and quality scores. Ion Torrent has partnered with Partek, CLC Bio, and DNAStar to enable their software to analyze data from the PGM.

A "web store" that Ion Torrent plans to open at launch will enable customers to purchase the software, as well as the instrument itself and consumables. In addition, the company will have a wiki where customers can download all supported protocols. This will also feature a section where users can upload their own protocols, and there will be a user discussion forum as well.

Initially, Ion Torrent will focus on targeted resequencing and microbial sequencing applications. Researchers have also shown an interest in using the system for quality control of libraries for high-throughput sequencers, Jain said, and the firm is currently evaluating this as a third initial application.
He said the company is neglecting counting applications such as ChIP-seq or RNA profiling for now, since these require larger numbers of reads than the system will initially support.

So far, Ion Torrent has placed its sequencer in several undisclosed labs, including, as previously reported, the Broad Institute. Later this year, the company plans to ship additional instruments to early-access customers and to formally launch the platform. Also, at the Association for Molecular Pathology meeting this month, a not-yet-disclosed early customer is scheduled to present data generated on the system.

Have topics you'd like to see covered in In Sequence? Contact the editor at jkarow [at] genomeweb [.] com

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